Required Input Parameters:
--------------------------
ligands (file): dataset of prepared ligands posed in the protein active site.
protein (file): dataset of the prepared protein structure.
Outputs:
--------
out (.oedb file): file of the protein-ligand complexes with parameters.
"""
# Locally the floe can be invoked by running the terminal command:
# python floes/LigReadPrep.py --ligands ligands.oeb --protein protein.oeb --out prod.oeb
job.classification = [['Molecular Dynamics']]
# job.uuid = "372e1890-d053-4027-970a-85b209e4676f"
job.tags = [tag for lists in job.classification for tag in lists]
# Ligand setting
iligs = DatasetReaderCube("LigandReader", title="Ligand Reader")
iligs.promote_parameter("data_in",
promoted_name="ligands",
title="Ligand Input Dataset",
description="Ligand Dataset")
ligset = LigandSetting("LigandSetting", title="Ligand Setting")
ligset.set_parameters(lig_res_name='LIG')
chargelig = ParallelLigandChargeCube("LigCharge", title="Ligand Charge")
chargelig.promote_parameter('charge_ligands',
promoted_name='charge_ligands',
description="Charge the ligand or not",
# PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall OpenEye be
# liable for any damages or liability in connection with the Sample Code
# or its use.
from floe.api import WorkFloe
from cuberecord import (DatasetReaderCube,
DatasetWriterCube)
from {{cookiecutter.module_name}} import MyCube
# Declare and document floe
my_floe = WorkFloe('my_floe', title="My Floe")
my_floe.description = "Outputs the input records unchanged unless the parameter is set to false, in which case nothing " \
"is outputted"
my_floe.classification = [["Examples"]]
my_floe.tags = ["Examples", "I didn't edit the tags"]
# Declare Cubes
input_cube = DatasetReaderCube('input_cube')
switch_cube = MyCube('switch_cube')
output_cube = DatasetWriterCube('output_cube')
# Add cubes to floe
my_floe.add_cube(input_cube)
my_floe.add_cube(switch_cube)
my_floe.add_cube(output_cube)
# Promote parameters
input_cube.promote_parameter('data_in', promoted_name='in', title='Input data set of records')
switch_cube.promote_parameter('switch', promoted_name='switch', title="Switch controlling Output")
output_cube.promote_parameter('data_out', promoted_name='out', title='Output File of Molecules')
#!/usr/bin/env python
from cubes.input_cubes import Test
from cubes.compute_cubes import ParallelFastROCSRanking, AccumulateRankings
from cubes.output_cubes import TextRankingOutputCube
from floe.api import WorkFloe, CubeGroup
from floe.api import OEMolIStreamCube
from floe.api import OEMolOStreamCube, FileOutputCube
# Declare Floe, add metadata for UI
job = WorkFloe('FastROCS Test Floe')
job.classification=[['Test']]
job.tags=[['yippee ki yay mf']]
job.title='test FastROCS Server'
job.description = """
Read a molecule query and return the FastROCS Server Results
"""
input_cube = Test('input')
request_cube = ParallelFastROCSRanking('request_cube')
request_cube.promote_parameter('url', promoted_name='url')
accu_cube = AccumulateRankings('accu')
accu_cube.promote_parameter('url', promoted_name='url')
output_cube = TextRankingOutputCube('results_output')
output_cube.promote_parameter('name', promoted_name='name')
job.add_cubes(input_cube, request_cube, accu_cube, output_cube)
input_cube.success.connect(request_cube.data_input)
# THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED. OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT
# NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
# PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall OpenEye be
# liable for any damages or liability in connection with the Sample Code
# or its use.
from floe.api import WorkFloe
from orionplatform.cubes import DatasetReaderCube, DatasetWriterCube
from am1bcc_charge.am1bcc_charge import AM1BCCCharge
# Declare and document floe
job = WorkFloe("am1bcc_charge", title="am1bcc charge")
job.description = ("AM1BCC Charge")
job.classification = [["Charge"]]
job.tags = ["Charge"]
# Declare Cubes
input_cube = DatasetReaderCube("input_cube")
charge_cube = MyCube("charge_cube")
output_cube = DatasetWriterCube("output_cube")
# Add cubes to floe
job.add_cube(input_cube)
job.add_cube(charge_cube)
job.add_cube(output_cube)
# Promote parameters
input_cube.promote_parameter("data_in",
promoted_name="in",
title="Input data set of records")
